[gmx-users] Cannot minimiza - vdwradii.dat ???

[Steven Neumann]

On Thu, Nov 15, 2012 at 2:35 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> I will. Thank you.
>
> Steven
>
> On Thu, Nov 15, 2012 at 2:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 11/15/12 9:03 AM, Steven Neumann wrote:
>>>
>>> On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>> On 11/15/12 8:41 AM, Steven Neumann wrote:
>>>>>
>>>>>
>>>>> Dear Gmx Users,
>>>>>
>>>>> I am trying to run simulations of protein and FE(2+) atoms. I placed
>>>>> them randomly around the protein, solvated the system and tried to
>>>>> minimize. After grompp, I tried mdrun:
>>>>>
>>>>> Stepsize too small, or no change in energy.
>>>>> Converged to machine precision,
>>>>> but not to the requested precision Fmax < 1000
>>>>>
>>>>> Double precision normally gives you higher accuracy.
>>>>> You might need to increase your constraint accuracy, or turn
>>>>> off constraints alltogether (set constraints = none in mdp file)
>>>>>
>>>>> Steepest Descents converged to machine precision in 62 steps,
>>>>> but did not reach the requested Fmax < 1000.
>>>>> Potential Energy  = -7.2573600e+05
>>>>> Maximum force     =  5.7863950e+05 on atom 756
>>>>> Norm of force     =  3.5862925e+03
>>>>>
>>>>> I tried different stepsizes, constarint = none etc but never converged
>>>>> to requested Fmax < 1000
>>>>>
>>>>> When I try NVT:
>>>>>
>>>>> Fatal error:
>>>>> 2 particles communicated to PME node 0 are more than 2/3 times the
>>>>> cut-off out of the domain decomposition cell of their charge group in
>>>>> dimension x.
>>>>> This usually means that your system is not well equilibrated.
>>>>>
>>>>>
>>>>> So the problem is with minimization.
>>>>>
>>>>> My question: Can it be the problem of not specified vdwradius of my
>>>>> FE(2+) in vdwradii.dat ? I mean, can ater molecules overlap with
>>>>> Ferrous and thus minimization does not converge?
>>>>>
>>>>
>>>> The problem is unrelated to vdwradii.dat, which is only used for neighbor
>>>> searching with genbox.  mdrun tells you there is a problem with atom 756.
>>>> What is it?  What is it interacting with?  That's how you trace the
>>>> problem.
>>>>
>>>> -Justin
>>>>
>>>
>>> This is Fe(2+) - from trjactory it can be observed that it collides
>>> with negatively charged oxygen from my other small molecule. Are you
>>> sure that vdwradii.dat wont solve it while placing molecules using
>>> genbox and then solvating. The vdw radius of Fe(2+) is 2 A. Would you
>>> suggest something?
>>>
>>
>> Try it and see.  If genbox doesn't find a radius, it uses a default value,
>> which is specified with -vdwd on the command line, so modifications to
>> vdwradii.dat are not strictly necessary, but a more explicit command might
>> be.
>>
>> -Justin

If change -vdwd to 0.2 it will affect slo water molecules which is not
desirable. Shall I just copy vdwradii.dat to my working directory and
add:


???  FE    0.20

Will that change it?

Steven

>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists